2.6. Bacteria (Fecal Coliform)

2.6.1. Description and Significance

2.6.1.1. Human bacteria, wastewater treatment, and the Clean Water Act

The human body is a complicated ecosystem that includes beneficial microorganisms such as bacteria, yeasts, and viruses on our skin, in our mucous membranes, and in our intestines.  Collectively, these microorganisms are called the ’human microbiome’ (NIH 2019). While a first reaction of many people upon learning this is “yuck,” it is well established that many of the microbes we harbor are beneficial and healthy for us, including their roles in digestion and combatting infectious disease pathogens.  The human digestive tract alone is home to about 10-100 trillion microorganisms.  Thus, feces has a very high density of microbes.  In addition to the non-disease-causing bacteria and viruses, feces from people infected with a variety of disease-causing microbes also contain the infectious disease pathogens.  Thus, human waste can contain various pathogens from infected individuals, so sewage wastewater is treated to remove these microorganisms before being released back into natural waters.

Over time, the standards for sewage treatment have become ever more stringent, particularly with the passage of the clean water act in 1977 (FAS 2019). This law required the nation’s publicly owned sewer systems to remove 90% of the solid matter, and to disinfect the effluent (Shabecoff 1988), which was usually done with chlorine, to protect streams and rivers. The COJ passed Environmental Protection Board (EPB) Rule 3 to improve water quality in Duval County (1987), which led to a phase-out of the existing but less reliable local wastewater treatment plants, many of which were unable to meet the higher standards. Consolidation into larger regional treatment plants helped meet the higher standards.

2.6.1.2. Fecal coliform as indicator organisms

Measurement of the effectiveness of wastewater treatment has historically involved the measurement of fecal coliform bacteria, among other water quality parameters. Fecal coliform bacteria are essentially indicator organisms that provide evidence of whether human waste and therefore associated pathogens, such as bacteria and viruses, are being sufficiently removed by wastewater treatment. Relatively few coliform bacteria are pathogenic themselves. One shortcoming of using fecal coliform bacteria as an indicator of wastewater treatment is that some species of fecal coliform bacteria can grow and multiply in sediment long after the initial wastewater discharge occurred (Anderson et al. 2005), so a high fecal coliform reading may not indicate an active, current discharge of untreated wastewater.

Sources of fecal coliform bacteria in natural waters include wastewater treatment facility outflows, but these are only one type of many potential sources. Fecal coliform bacteria reach the river from natural sources such as wildlife. Other sources include sanitary sewer overflows, domestic animal and pet contamination, human contamination from failing septic systems, runoff, and agricultural wastes from intensive animal farming and pasturelands

2.6.1.3. Fecal coliform criteria for recreational waterbodies

The mainstem and tributaries of the LSJR are designated as Class III recreational waters, suitable for ‘fish consumption, recreation, propagation and maintenance of a healthy, well-balanced population of fish and wildlife.’ Until recently, the Florida fecal coliform exceedance criteria standards for recreational waters stated that fecal coliform counts (CFU) per 100 mL should adhere to all three of the following:

  1. not exceed a monthly average of 200 (requires 10 samples in a 30-day period)
  2. not exceed 400 in 10% of samples
  3. not exceed 800 on any one day

These fecal coliform criteria for recreational water quality were based on 1976 EPA recommendations (EPA 1976), which were based on studies that found an increase in gastrointestinal illnesses after swimming in waterways that had about 400 coliform bacteria or more per 100 milliliters of water (EPA 1986). For protective measures, the number was halved to 200 fecal coliform bacteria per 100 milliliters as a threshold value for the monthly average value in the criteria.  In 1986, based on additional studies, the EPA shifted away from fecal coliform to recommending that E. coli and enterococci be used as the indicator organisms for human sewage (EPA 1986) and in 2012 the U.S. EPA refined the 1986 recommendations for using E. coli and enterococci (EPA 2012a). The FDEP has recently changed standards to fit the 2012 recommendations (see below).

2.6.1.4. The focus on tributaries of the LSJR

Under the FDEP “River-at-a-Glance” program through 2008, the mainstem of the LSJR (at several sites from Welaka to Arlington (in Jacksonville), was found to be largely in compliance for fecal coliform (Appendix 2.6.1). Since the tributaries were largely not in compliance, and the mainstem was in compliance, the focus became the tributaries.  Since the tributaries are the waterbodies impaired for fecal bacteria, they are the focus of the rest of this section.

2.6.2Current Status

STATUS: Unsatisfactory

TREND: Conditions Unchanged

Seventy-five tributaries are impaired for fecal coliform (FDEP 2016). Of these, thirty-six tributaries have final TMDLs for fecal coliform, and fecal coliform BMAPs are in place for twenty-five of them (Table 2.1).

Table 2.1 LSJRB Tributaries with final fecal coliform TMDLs.  Tributaries with BMAPs are indicated in bold.

Big Davis CreekCraig CreekGreene CreekLittle Black CreekNewcastle CreekSherman Creek
Big Fishweir CreekDeep Bottom CreekGreenfield CreekMcCoy CreekOpen CreekStrawberry Creek
Block House CreekDeer CreekGrog BranchMill CreekOrtega RiverTerrapin Creek
Butcher Pen CreekDurbin CreekHogan CreekMiller CreekPeters CreekTrout River (Middle and Lower)
Cedar RiverFishing CreekHopkins CreekMiramar CreekPottsburg CreekWills Branch
Cormorant BranchGoodbys CreekJulington CreekMoncrief CreekRibault RiverWilliamson Creek

2.6.2.1. Percent exceedances are far from goals

As noted above, Florida statute has required that monthly averages must be calculated from at least 10 samples per 30 days.  However, most impaired tributaries do not undergo fecal coliform testing that frequently. Therefore, the criterion stating that no more than 10% of samples may exceed 400 CFU/100 mL (criterion #2 above) was the metric being used by the FDEP to assess improvement, and has been the goal.  No tributary has reached this goal, and most are not even close (Table 2.2A), with 23% exceedance as the lowest value, and 95% as the highest value for the most recent 7.5-year period (2010-2017).  When comparing the three most recent 7.5-year averages (Table 2.2A), 21 of the tributaries show no substantial changes in percent exceedances, and 2 of the tributaries have increased by more than 10 percentage points (Table 2.2A; pink). Some progress has been made in Miramar, and Deep Bottom Creeks, which have exceedance percentages that have decreased 10 percentage points (Table 2.2A; blue), but are still far from compliance.

2.6.2.2. Magnitude of exceedances are far from goals but have made progress

While the percent exceedances for the majority of the tributaries have made no progress in declining, there has been considerable success in bringing down the magnitude of the exceedances when the 1996-2003 and 2010-2014 data sets are compared (last two columns in Table 2.2A). Ideally, the fecal indicator bacteria counts will continue to decrease to where the tributaries are no longer exceeding the 10% percent exceedance maximum as well as the single day criterion (criterion #3 above) of 800 fecal coliform on any day.

Table 2.2A Fecal coliform exceedances of LSJRB Tributaries.  Percent exceedances show 7.5-year rolling averages for the last four periods that data is publicly available for, with the most recent time-period in bold.  Pink indicates tributaries whose exceedances increased by at least 10 percentage points and light blue indicates tributaries that have decreased by at least 10 percentage points when comparing the first time-period to the last time-period.  Exceedance median shows the magnitude of exceedances for two separate time-periods (TMDL period is 1996-2003; BMAP period is 2010-2014).

Table of fecal coliform exceedances of the LSJRB

2.6.3. Progress and Outlook

2.6.3.1. BMAPs, Walk the WBID, and activities to address fecal coliform exceedances

Generally, Basin Management Action Plans (BMAPs) lay out projects and plans intended to reduce loading of the identified pollutant, to be executed by the key responsible parties. For fecal coliform BMAPs in this set of 25 tributaries, the responsible parties are COJ, JEA, the Florida Department of Transportation, the Florida Department of Health, Naval Station Mayport, and other relevant municipalities including the Cities of Atlantic Beach, Jacksonville Beach, and Neptune Beach. FDEP also plays a role in implementation of BMAP projects. For these 25 tributaries, a coordinating body called the Tributaries Assessment Team organizes these groups in terms of information review and taking next steps.

Because the primary sources of fecal coliform are stormwater, wastewater, and septic tanks, the projects undertaken to reduce fecal coliform usually address these types of water streams. Examples of projects undertaken to reduce fecal coliform include wastewater infrastructure improvements, removal of illicit wastewater connections to waterbodies, and septic tank phase-out and replacement by connection to municipal sewage services. Dozens of projects on these tributaries have been completed since the start of these BMAPs.

Yet, despite these projects, many of which have certainly decreased the amount of human waste entering the watershed, the above results indicate that the tributaries remain significantly impaired for fecal coliform. Stakeholders have conducted an intensive effort to investigate sources of fecal coliform. For the Tributaries I group, Maps on the Table and Walk the WBID (Water Body Identification Number) exercises were conducted in 2014. Maps on the Table is a process by which stakeholders with local knowledge of the water body meet and review a map of the WBID to identify possible sources and issues needing further study. These were followed by Walk the WBID days, in which stakeholders actually hike along the banks of the water body to observe and note potential problem areas. After these events, follow-up activities were identified, and both long-term and short-term solutions to this problem are being sought. The Tributaries II group was examined by slightly scaled-back Maps on the Table and Walk the WBID exercises in April 2015 by a coordinated inter-agency effort. During these walks, a few short-term issues were discovered and quickly addressed by the appropriate agency. Future long-term efforts generally involve maintenance activities, modified or expanded inspections, educational outreach, and basin-specific cleanup strategies.

2.6.3.2. Rule changes: Switching from fecal coliform testing to E. coli and Enterococcus testing

As explained above, Florida’s fecal coliform criteria were based on 1976 U.S. EPA recommendations, which have since been updated twice by the U.S. EPA.  Recently, new bacteria criteria to replace the fecal coliform standards were developed by FDEP.  These criteria adopt Recreational Water Quality Criterion (RWQC) promulgated by U.S. EPA in 2012 (EPA 2012b). This new RWQC is specific for E. coli and enterococci, rather than fecal coliform, a broader class of organisms.  It was found that enterococci and E. coli are superior indicators of fecal contamination than simply fecal coliform, because a) the correlation between swimmer disease and bacteria levels is stronger for these specific bacteria than for the larger class of fecal coliform bacteria (EPA 2012a), and b) fecal coliform testing can also measure the presence of some bacteria that did not come from feces (Jin et al. 2004). E. coli will now be used for fresh waters, and enterococci will be used for saline waters.

Recent data for 10 tributaries using these new criteria are compared to data for the old criteria (Table 2.2B). Percent exceedances of fecal indicator bacteria using the new criteria are noticeably lower for 7 of the tributaries and higher for 2 of the tributaries compared to the larger fecal coliform data set (Table 2.2B). Future editions of this Report will expand on these new criteria as Florida incorporates them and as more data on E. coli and enterococci come available.

Table 2.2B Fecal coliform exceedances compared to E. coli and enterococci exceedances.  Percent exceedances for old criteria encompass 1/1/2010 – 6/30/2017, and for new criteria are from 2016 and 2017 only.  Pink indicates tributaries whose exceedances are at least 20 percentage points greater and light blue indicates tributaries whose exceedances are at least 20 percentage points lower when comparing the new criteria to the old criteria.

Table 2.2B Fecal coliform exceedances compared to E. coli and enterococci exceedances.

2.6.3.3. Source tracking: New tools to track the sources of fecal coliform

As discussed above, fecal coliform, E. coli, and Enterococcus are the bacteria that either have been (fecal coliform) or are currently (E. coli, and enterococci) being tested for in waterways to determine impairment.  Significant effort has been put forth to determine the source of the elevated levels of these bacteria (broken sewer pipes, septic tanks, sanitation sewer overflows) in many tributaries, often times without finding any “smoking gun.” Since these bacteria can come from a variety of animals, not just humans, there is a possibility that elevated levels of these bacteria in these bacteria-impaired waterways, actually come from other animals, and not humans.  To address this, FDEP has been using additional methods to see not only if the bacteria come from humans, since human waste has a higher health risk than wildlife and pet wastes, but also to determine if the bacteria are recent additions (from raw human sewage) to the waterway.  This approach, called source tracking, seeks to determine whether or not the original source of the bacteria was human, and if so, if the bacteria might be from raw human waste.  To do this, a variety of techniques, from something like a scientist’s “tool box”, are being employed as follows (DEP 2018d).

Genetic Signatures of human-associated bacteria to detect raw human waste – A technique called qPCR (quantitative polymerase chain reaction) is used to detect and quantify genetic sequences, called “HF-183” that are only in Bacteroides bacteria and most commonly from humans (Ahmed et al. 2016).  These Bacteroides die when they are exposed to oxygen, so when they leave the human body, they will not be able to live for a long period of time in the environment.  And, these Bacteroides are killed during wastewater treatment.  So, a water sample that tests positive for HF-183 has contributions from recent raw human waste, which would be considered the source. There are minor exceptions to this rule so results are reviewed along with multiple lines of evidence such as other tracers of wastewater and knowledge about the activities in the watershed to guide interpretations.

Sucralose – Sucralose is a chemical used as an artificial sweetener (for example, Splenda). Sucralose is not broken down by the body or by wastewater treatment.  Therefore, water samples can also be analyzed for sucralose, and if it is present, then the waterway includes some type of wastewater, either treated wastewater effluent (from septic tanks or wastewater treatment plants), or raw human waste.  In other words, whether the wastewater was treated or not is unknown.

Acetaminophen and Naproxen – Acetaminophen and naproxen are chemicals used as a pain reliever (an example of acetaminophen is Tylenol).  When someone takes acetaminophen or naproxen, all of it is not broken down by the body, and so some is released as waste.  Acetaminophen and naproxen are removed from wastewater during treatment processes (septic tank or wastewater treatment plant), so acetaminophen or naproxen in a water sample indicates presence of raw human waste.  

By combining the source tracking results of the different analyses, scientists can begin to determine 1) whether the fecal indicator bacteria in a tributary are from humans or not, 2) whether the waterbody has been impacted by treated or untreated sewage, and 3) whether the introduction of the fecal bacteria into the waterway was recent or not.  For example, if a water sample has high levels of fecal bacteria, high levels of the HF-183 human-Bacteroides genetic signature, and high levels of acetaminophen, then it is clear that raw human wastewater is present, so the source/location of the human waste must be found and remedied.  If a water sample has high levels of fecal bacteria, but no HF-183 human-Bacteroides genetic signature, and no sucralose or acetaminophen, then raw human wastewater is not suspected.  In this case, the water body may not be a priority, as the source of the fecal coliform may be from wildlife, or the fecal coliform may have come from humans in the past, but is now just growing and living in the tributaries, with no associated human pathogens present, and thus is not an indication of a health risk.  This approach is much more complicated than explained here, and sometimes even extensive analysis does not reveal the source, which necessitates continued sampling and analysis.

2.6.3.4. Using the source tracking tools in bacteria-impaired waters

In 2018, FDEP utilized these new source tracking methods to find high-risk sources of fecal bacteria in tributaries of the Lower St. Johns River (Figure 2.27).  Samples in 2018 that exceeded the fecal bacteria ten percent threshold value designated as criteria in the standard were analyzed for the HF-183 human-Bacteroides genetic signature.  If the signature was present, then the sample was considered confirmed for untreated human waste.  If the signature was not detected, then the sample was analyzed for bacterial genetic signatures from ruminants (livestock such as cows and sheep, etc.) using a similar qPCR technique.  If there was no indication that ruminant waste was present, then genetic signatures from bacteria found in certain types of birds were tested for (positive results for bird waste bacteria would indicate that wildlife contribute to the bacterial load). Of 32 waterbodies tested, 15 were confirmed to have untreated human waste in 2018, 12 are suspected to have had untreated human waste, with one of those waterbodies also having ruminant waste, and for 5 sites, the source is still unknown (Figure 2.27)

Figure 2.27 Results of 2018 BMAP Watersheds Source Investigations. Circles represent combined results for each waterbody, not a specific location in the waterbody (DEP 2018a).
Figure 2.27 Results of 2018 BMAP Watersheds Source Investigations. Circles represent combined results for each waterbody, not a specific location in the waterbody (DEP 2018a).

2.6.4. Conclusion

Fecal bacteria are a significant problem in the tributaries of the LSJRB, and considerable effort is being made to remedy this problem by way of the state TMDL, BMAP, and Source Tracking processes. Many tributaries with elevated fecal bacteria levels have undergone large reductions, which is an encouraging sign. However, despite making large reductions, actual fecal bacteria levels in many tributaries are persistently higher than the current rules for the water quality criteria, and the percent exceedances are very high.  Results from the new criteria where E. coli and enterococci are analyzed may be showing lower exceedances in some instances compared to the historic fecal coliform criteria.  As agencies obtain more data with the new criteria, continue source tracking, and continue to invest in improving sewage infrastructure, our understanding of fecal bacteria in the LSJRB should become clearer, and reductions in this problem should continue to be made.

Water Quality, Fisheries, Aquatic Life, & Contaminants